Construction of a chromosome‐level genome and variation map for the Pacific oyster <i>Crassostrea gigas</i>

Qi, Hongsheng; Li, Li; Zhang, Guofan

doi:10.1111/1755-0998.13368

Cited by 64 publications

(46 citation statements)

References 88 publications

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“…57.3% (535.9 Mb) of the OE_Roslin_V1 assembly was identified as repeats (Figure 2a), which falls in a similar range to recently published C. gigas genome assemblies (reported as 43% by and 57.2% by Qi et al (2021)). A large majority of repeats, comprising 37.65% of the genome, were annotated as unclassified (Figure 2a).…”

Section: Genome Annotationsupporting

confidence: 84%

Chromosome level reference genome for European flat oyster (Ostrea edulis L.)

Gundappa

Peñaloza

Regan

et al. 2022

Preprint

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The European flat oyster (Ostrea edulis L.) is a bivalve naturally distributed across Europe that was an integral part of human diets for centuries, until anthropogenic activities and disease outbreaks severely reduced wild populations. Despite a growing interest in genetic applications to support population management and aquaculture, a reference genome for this species is lacking to date. Here we report a chromosome-level assembly and annotation for the European Flat oyster genome, generated using Oxford Nanopore, Illumina, Dovetail OmniC™ proximity ligation and RNA sequencing. A contig assembly (N50: 2.38Mb) was scaffolded into the expected karyotype of 10 pseudo-chromosomes. The final assembly is 935.13 Mb, with a scaffold-N50 of 95.56 Mb, with a predicted repeat landscape dominated by unclassified elements specific to O. edulis. The assembly was verified for accuracy and completeness using multiple approaches, including a novel linkage map built with ddRAD-Seq technology, comprising 4,016 SNPs from four full-sib families (8 parents and 163 F1 offspring). Annotation of the genome integrating multi-tissue transcriptome data, comparative protein evidence and ab-initio gene prediction identified 35,699 protein-coding genes. Chromosome level synteny was demonstrated against multiple high-quality bivalve genome assemblies, including an O. edulis genome generated independently for a French O. edulis individual. Comparative genomics was used to characterize gene family expansions during Ostrea evolution that potentially facilitated adaptation. This new reference genome for European flat oyster will enable high-resolution genomics in support of conservation and aquaculture initiatives, and improves our understanding of bivalve genome evolution.

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Section: Genome Annotationsupporting

confidence: 84%

Chromosome level reference genome for European flat oyster (Ostrea edulis L.)

Gundappa

Peñaloza

Regan

et al. 2022

Preprint

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“…Considering the two species are closely related with a divergence time of only about 2.7 My ( Ren et al 2010 ) and regarded as subspecies by some ( Wang et al 2010 ), we used the reference genome of C. gigas to calculate nucleotide diversity of C. angulata due to the lack of a reference genome for C. angulata . Although reference genome would affect nucleotide diversity estimates, the mapping rate for C. angulata reads was only slightly lower than that for C. gigas ( Qi et al 2021 ). We detected candidate regions with selection signatures by screening the genome for regions with the largest differences in θπ ratio ( θπ , Ca / θπ , Cg , bottom and top 5%) and fixation index ( F ST , top 5%) values ( Weir and Cockerham 1984 ).…”

Section: Methodsmentioning

confidence: 88%

Noncoding Variation and Transcriptional Plasticity Promote Thermal Adaptation in Oysters by Altering Energy Metabolism

Zhang

et al. 2021

Molecular Biology and Evolution

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Genetic variation and phenotypic plasticity are both important to adaptive evolution. However, how they act together on particular traits remains poorly understood. Here, we integrated phenotypic, genomic, and transcriptomic data from two allopatric but closely related congeneric oyster species, Crassostrea angulata from southern/warm environments and Crassostrea gigas from northern/cold environments, to investigate the roles of genetic divergence and plasticity in thermal adaptation. Reciprocal transplantation experiments showed that both species had higher fitness in their native habitats than in non-native environments, indicating strong adaptive divergence. The southern species evolved higher transcriptional plasticity, and the plasticity was adaptive, suggesting that increased plasticity is important for thermal adaptation to warm climates. Genome-wide comparisons between the two species revealed that genes under selection tended to respond to environmental changes and showed higher sequence divergence in noncoding regions. All genes under selection and related to energy metabolism exhibited habitat-specific expression with genes involved in ATP production and lipid catabolism highly expressed in warm/southern habitats, and genes involved in ATP consumption and lipid synthesis were highly expressed in cold/northern habitats. The gene for acyl-CoA desaturase, a key enzyme for lipid synthesis, showed strong selective sweep in the upstream noncoding region and lower transcription in the southern species. These results were further supported by the lower free fatty acid (FFA) but higher ATP content in southern species and habitat, pointing to significance of ATP/FFA trade-off. Our findings provide evidence that noncoding variation and transcriptional plasticity play important roles in shaping energy metabolism for thermal adaptation in oysters.

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“…So far, according to the data released by NCBI, a total of 80 mollusks genome have been published, of which 34 are from bivalves, 36 from gastropods, nine from cephalopods and one from polyplacophora. Note that ostreidae is one of the most studied families of bivalves (Peñaloza et al, 2021; Peng et al, 2020; Powell et al, 2018; Qi et al, 2021; Zhang et al, 2012), and the economic bivalves with published genomes mainly include oyster, scallop, clam, mussel and razor clam species. These genomes of mollusks show variable sizes.…”

Section: Introductionmentioning

confidence: 99%

Chromosome‐level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oysterCrassostrea ariakensis

Chen

Yu³

et al. 2021

Molecular Ecology Resources

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The Jinjiang oyster Crassostrea ariakensis, naturally distributing in estuarine regions with low salinity, is an important economic and ecological species in China. However, studies on its genomics and population genetics remain lacking. Here, we assembled the chromosome‐level genome of a female C. ariakensis and re‐sequenced 261 individuals from five locations in China representing three typical habitats. The C. ariakensis genome was 662.9 Mb with contig N50 length of 5.9 Mb using PacBio HiFi‐CCS long reads, and 99.83% sequences were anchored onto 10 pseudochromosomes using Hi‐C data. A total of 26,354 protein‐coding genes were predicted. We identified three significantly expanded gene families which are closely associated with osmotic pressure regulation, including CDO, SLC13 and SDR. Population structure analysis revealed that the C. ariakensis from five locations were clustered into three typical groups (northern, southern and Shanghai) (K = 3) and their phylogenetic relationship was consistently correlated to their geographical distribution. Furtherly, the differentiation between northern and southern groups was clearly demonstrated by estimated population differentiation coefficient (FST = 0.1154), and the PSMC distribution showed the two groups of effective population size separated at 0.1 Ma. Meanwhile gene flow from southern to Shanghai was detected. Selective sweep analysis between northern and southern group detected genes associated with heat response and salinity adaptation. This study could provide valuable genomic resources and information for further research on the molecular evolution, genetic breeding, biological function and evolutionary adaptation of C. ariakensis.

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Construction of a chromosome‐level genome and variation map for the Pacific oyster Crassostrea gigas

Cited by 64 publications

References 88 publications

Chromosome level reference genome for European flat oyster (Ostrea edulis L.)

Chromosome level reference genome for European flat oyster (Ostrea edulis L.)

Noncoding Variation and Transcriptional Plasticity Promote Thermal Adaptation in Oysters by Altering Energy Metabolism

Chromosome‐level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oysterCrassostrea ariakensis

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